[Freesurfer] R: Re: R: Re: Import FS data to FSL

Hi list and Anastasia. Thank you very much. mri_annotatiion2label works fine. Becouse I should run this command: label2surf -s <surface> -o <outputsurface> -l <labels> -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files I should provide also surface file relatively to each .label previously created with mri_annotatiion2label. How can I do? Thanks,

Stefano

----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 26-set-2013 0.57 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL

Try mri_annotation2label.

On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:

For FSL guide:

I should transforms a group of labels into a surface

Usage:

label2surf -s <surface> -o <outputsurface> -l <labels>

Compulsory arguments (You MUST set one or more of):

    -s,--surf       input surface

    -o,--out        output surface

    -l,--labels     ascii list of label files

Optional arguments (You may optionally specify one or more of):

    -v,--verbose    switch on diagnostic messages

    -h,--help       display this message

but I should create a lh/rh.frontal.label and use it for label2surf.

With mdi_binarize I can create .nii.gz but no .label. Is that correct?

How I can do it?

Thanks,

Stefano

----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import FS data to FSL

1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL.

On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:

...

Hi list,

I have 2 questions, please.

1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)?

2-I'd like to export cortical masks from FS to FSL.

An option is mri_binarize but this way failed in probtrackx (fsl). FSL list have advised me that I should use label2surf command to convert label to surface files.

Where could find the .label (according to FreeSurferColorLUT.txt) to build mask of frontal, parietal, motor, sensor, temporal and occipital lobes?

Do you have other ways that you advise me?

Thanks,

Stefano

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